SMTL ID : 3wzp.1

Crystal structure of the core streptavidin mutant V21 (Y22S/N23D/S27D/Y83S/R84K/E101D/R103K/E116N) complexed with iminobiotin long tail (IMNtail) at 1.2 A resolution

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.20 Å

Oligo State

homo-tetramer

Ligands

4 x ZOF: 6-({5-[(2E,3aS,4S,6aR)-2-iminohexahydro-1H-thieno[3,4-d]imidazol-4-yl]pentanoyl}amino)hexanoic acid(Non-covalent)

ZOF.1: 19 residues within 4Å: Chain A: D.13, L.15, D.17, Y.33, S.35, V.37, G.38, N.39, W.69, A.76, S.78, T.80, W.98, L.100, S.102, L.114, D.118 Chain C: W.110 Ligands: ZOF.5 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:W.69, A:W.69, A:W.69, A:L.114 Hydrogen bonds: A:Y.33, A:N.39, A:S.78, A:S.78, A:W.98 Water bridges: A:D.17, A:S.35 Salt bridges: A:D.17, A:D.118 ZOF.4: 21 residues within 4Å: Chain B: D.13, L.15, D.17, Y.33, S.35, V.37, G.38, N.39, A.40, W.69, A.76, S.78, T.80, W.98, L.100, S.102, L.114, D.118 Chain D: W.110, K.111 Ligands: ZOF.7 14 PLIP interactions: 14 interactions with chain B Hydrophobic interactions: B:A.40, B:W.69, B:W.69, B:L.114 Hydrogen bonds: B:Y.33, B:N.39, B:S.78, B:S.78, B:W.98 Water bridges: B:D.17, B:S.35 Salt bridges: B:D.13, B:D.17, B:D.118 ZOF.5: 19 residues within 4Å: Chain A: W.110 Chain C: D.13, L.15, D.17, Y.33, S.35, V.37, G.38, N.39, W.69, A.76, S.78, T.80, W.98, L.100, S.102, L.114, D.118 Ligands: ZOF.1 13 PLIP interactions: 13 interactions with chain C Hydrophobic interactions: C:W.69, C:W.69, C:W.69, C:L.114 Hydrogen bonds: C:Y.33, C:N.39, C:S.78, C:S.78, C:W.98 Water bridges: C:D.17, C:S.35 Salt bridges: C:D.17, C:D.118 ZOF.7: 19 residues within 4Å: Chain B: W.110 Chain D: D.13, L.15, D.17, Y.33, S.35, V.37, G.38, N.39, W.69, A.76, S.78, T.80, W.98, L.100, S.102, L.114, D.118 Ligands: ZOF.4 14 PLIP interactions: 14 interactions with chain D Hydrophobic interactions: D:W.69, D:W.69, D:W.69, D:L.114 Hydrogen bonds: D:Y.33, D:Y.33, D:N.39, D:S.78, D:S.78, D:W.98 Water bridges: D:D.17, D:V.37 Salt bridges: D:D.17, D:D.118

5 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 3 residues within 4Å: Chain A: E.34, E.41, S.42 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.34, A:S.42 Water bridges: A:E.34, A:A.40 GOL.3: 7 residues within 4Å: Chain A: V.45, K.70, N.71, N.72 Chain B: D.26, R.49, S.52 8 PLIP interactions: 5 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:S.52, B:S.52, A:K.70, A:N.72 Water bridges: B:R.49, B:R.49, B:S.52, A:K.70 GOL.6: 7 residues within 4Å: Chain C: D.26, G.27, R.49, S.52 Chain D: K.70, N.71, N.72 7 PLIP interactions: 4 interactions with chain C, 3 interactions with chain D Hydrogen bonds: C:R.49, C:S.52, C:S.52, D:K.70, D:N.72 Water bridges: C:S.52, D:K.70 GOL.8: 6 residues within 4Å: Chain C: K.70, N.71, N.72 Chain D: D.26, R.49, S.52 6 PLIP interactions: 4 interactions with chain D, 2 interactions with chain C Hydrogen bonds: D:D.26, D:R.49, D:S.52, D:S.52, C:K.70, C:N.72 GOL.9: 3 residues within 4Å: Chain D: S.59, V.87, G.88 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:G.88

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kawato, T. et al., Structure-based design of a streptavidin mutant specific for an artificial biotin analogue. J.Biochem. (2015)

Release Date

2015-02-18

Peptides

Streptavidin: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Streptavidin

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